Shikimic acid (ECMDB03070) (M2MDB000477)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (4)Transporters (5)XML
Proteins (1046)
Record Information
Version2.0
Creation Date2012-05-31 13:57:48 -0600
Update Date2015-09-13 12:56:12 -0600
Secondary Accession Numbers
  • ECMDB03070
Identification
Name:Shikimic acid
DescriptionShikimic acid, more commonly known as its anionic form shikimate, is an important biochemical intermediate in plants and microorganisms. Its name comes from the Japanese flower shikimi (
Structure
Thumb
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms:
  • (-)-Shikimate
  • (-)-Shikimic acid
  • L-Shikimate
  • L-Shikimic acid
  • Shikimate
  • Shikimic acid
  • Skikimate
  • Skikimic acid
Chemical Formula:C7H10O5
Weight:Average: 174.1513
Monoisotopic: 174.05282343
InChI Key:JXOHGGNKMLTUBP-HSUXUTPPSA-N
InChI:InChI=1S/C7H10O5/c8-4-1-3(7(11)12)2-5(9)6(4)10/h1,4-6,8-10H,2H2,(H,11,12)/t4-,5-,6-/m1/s1
CAS number:138-59-0
IUPAC Name:(3R,4S,5R)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid
Traditional IUPAC Name:(-)-shikimate
SMILES:O[C@@H]1CC(=C[C@@H](O)[C@H]1O)C(O)=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as shikimic acids and derivatves. These are cyclitols containing a cyclohexanecarboxylic acid substituted with three hydroxyl groups at positions 3, 4, and 5.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassAlcohols and polyols
Direct ParentShikimic acids and derivatves
Alternative Parents
Substituents
  • Shikimic acid or derivatives
  • Secondary alcohol
  • Polyol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxide
  • Hydrocarbon derivative
  • Carbonyl group
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:-1
Melting point:186 °C
Experimental Properties:
PropertyValueSource
Water Solubility:150 mg/mL at 21 oC [YALKOWSKY,SH & DANNENFELSER,RM (1992)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility206 g/LALOGPS
logP-1.7ALOGPS
logP-1.6ChemAxon
logS0.07ALOGPS
pKa (Strongest Acidic)4.1ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area97.99 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity38.96 m³·mol⁻¹ChemAxon
Polarizability15.75 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
3-Dehydro-shikimate + Hydrogen ion + NADPH <> NADP + Shikimic acid
Adenosine triphosphate + Shikimic acid <> ADP + Hydrogen ion + Shikimate 3-phosphate
Adenosine triphosphate + Shikimic acid <> ADP + Shikimate 3-phosphate
Shikimic acid + NADP <> 3-Dehydro-shikimate + NADPH + Hydrogen ion
Shikimic acid + NAD <> 3-Dehydro-shikimate + NADH + Hydrogen ion
NAD(P)<sup>+</sup> + Shikimic acid < NAD(P)H + 3-Dehydro-shikimate + Hydrogen ion
NADP + Shikimic acid < Hydrogen ion + NADPH + 3-Dehydro-shikimate
Shikimic acid + Adenosine triphosphate > Hydrogen ion + Shikimate 3-phosphate + ADP
Shikimic acid + NADP > 3-dehydroshikimate + NADPH
Adenosine triphosphate + Shikimic acid > ADP + Shikimate 3-phosphate
Shikimic acid + NAD(P)(+) > 3-dehydroshikimate + NAD(P)H
Quinate + NAD + NADP + Shikimic acid <> 3-Dehydroquinate + NADH + NADPH + Hydrogen ion + 3-Dehydro-shikimate
3-dehydroshikimate + Hydrogen ion + NADPH + 3-Dehydro-shikimate + NADPH > NADP + Shikimic acid
Shikimic acid + Adenosine triphosphate > Adenosine diphosphate + Hydrogen ion + shikimate 3-phosphate + ADP + Shikimate 3-phosphate
3 3-Dehydro-shikimate + Hydrogen ion + NADPH <> NADP + Shikimic acid
Adenosine triphosphate + Shikimic acid <> ADP + Hydrogen ion + Shikimate 3-phosphate
3 3-Dehydro-shikimate + Hydrogen ion + NADPH <> NADP + Shikimic acid
SMPDB Pathways:
Chorismate biosynthesisPW000816 ThumbThumb?image type=greyscaleThumb?image type=simple
Secondary Metabolites: Shikimate PathwayPW000985 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
  • Metabolic pathways eco01100
  • Phenylalanine, tyrosine and tryptophan biosynthesis ec00400
EcoCyc Pathways:
  • chorismate biosynthesis from 3-dehydroquinate PWY-6163
Concentrations
Find out more about how we convert literature concentrations.
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)splash10-0udj-0970000000-42465cd3f3e138b0bc12View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-0udi-0790000000-1100443abb8605953f58View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)splash10-00di-9450000000-e6ca954dc1a9c1cc4285View in MoNA
GC-MSGC-MS Spectrum - GC-MS (4 TMS)splash10-0udi-0491000000-49993b9b18e12b9461fcView in MoNA
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-0udi-0391000000-ddb2c574233062a911faView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0udj-0970000000-42465cd3f3e138b0bc12View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0udi-0790000000-1100443abb8605953f58View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-00di-9450000000-e6ca954dc1a9c1cc4285View in MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0udi-0491000000-49993b9b18e12b9461fcView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0a4i-4900000000-817f1ed3feb4c763285fView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positivesplash10-0092-7119400000-67b0989b5019a72e1016View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-01b9-1900000000-fd80f5e7f51d927e8e15View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-0a4i-9300000000-cf8a3148fd132540bf97View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-0a4i-9000000000-ed28bc20ae43473043c9View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-0a4i-9000000000-65249fc24f2de4acf2c7View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0a4i-9000000000-26dfc876ae35c2cdb845View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-006x-9600000000-3a5ab91754d9d837d8b4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-01b9-1900000000-6cba5b9b7c4891522045View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0a4i-9300000000-12d15a049b141a37f34eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0a4i-9000000000-ed28bc20ae43473043c9View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0a4i-9000000000-9864f7359ffed65d6ef0View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0a4i-9000000000-26dfc876ae35c2cdb845View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-006x-9600000000-3a5ab91754d9d837d8b4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-00di-7900000000-d77a830354efe8731a42View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-01vx-9700000000-d2060c544171987e3dcdView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-01vx-9500000000-baa64c3938f3d039c6e4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-00kf-9000000000-d5821372fd8a830dc962View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-00dl-9000000000-cb13aba83ba37150b931View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-01vo-9600000000-3433190ea61f16d92efdView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-022l-9600000000-60e85b9b59edb135e4c4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-0006-9000000000-58e1775d1e013c416201View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-1f370d2806fd8245ebfbView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-01vx-9600000000-d502f575cada8c0b5aeaView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-00dl-9400000000-d0ff38d5a290b8e8248dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-004i-0900000000-e6ca4ce5acb44dc23a74View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-004r-9700000000-18afe769b0ef5ba3fbdbView in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. Pubmed: 19561621
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • Liu Y, Xie MX, Jiang M, Wang YD: Spectroscopic investigation of the interaction between human serum albumin and three organic acids. Spectrochim Acta A Mol Biomol Spectrosc. 2005 Jul;61(9):2245-51. Pubmed: 15911418
  • Rose GA: Studies on the chemical nature of urinary chemiluminescence. Br J Urol. 1976 Feb;48(1):61-71. Pubmed: 5168
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Vijayendran, C., Barsch, A., Friehs, K., Niehaus, K., Becker, A., Flaschel, E. (2008). "Perceiving molecular evolution processes in Escherichia coli by comprehensive metabolite and gene expression profiling." Genome Biol 9:R72. Pubmed: 18402659
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Download (PDF)
External Links:
ResourceLink
CHEBI ID16119
HMDB IDHMDB03070
Pubchem Compound ID8742
Kegg IDC00493
ChemSpider ID8412
WikipediaShikimic acid
BioCyc IDSHIKIMATE
EcoCyc IDSHIKIMATE
Ligand ExpoSKM

Enzymes

Protein Details
1. Quinate/shikimate dehydrogenase
General function:
Involved in nucleotide binding
Specific function:
The physiological substrate is not known
Gene Name:
ydiB
Uniprot ID:
P0A6D5
Molecular weight:
31228
Reactions
L-quinate + NAD(P)(+) = 3-dehydroquinate + NAD(P)H.
Shikimate + NAD(P)(+) = 3-dehydroshikimate + NAD(P)H.
Protein Details
2. Shikimate kinase 1
General function:
Involved in shikimate kinase activity
Specific function:
Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate
Gene Name:
aroK
Uniprot ID:
P0A6D7
Molecular weight:
19538
Reactions
ATP + shikimate = ADP + shikimate 3-phosphate.
Protein Details
3. Shikimate kinase 2
General function:
Involved in shikimate kinase activity
Specific function:
Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate
Gene Name:
aroL
Uniprot ID:
P0A6E1
Molecular weight:
19151
Reactions
ATP + shikimate = ADP + shikimate 3-phosphate.
Protein Details
4. Shikimate dehydrogenase
General function:
Involved in nucleotide binding
Specific function:
Shikimate + NADP(+) = 3-dehydroshikimate + NADPH
Gene Name:
aroE
Uniprot ID:
P15770
Molecular weight:
29413
Reactions
Shikimate + NADP(+) = 3-dehydroshikimate + NADPH.

Transporters

Protein Details
1. Shikimate transporter
General function:
Involved in transporter activity
Specific function:
Specific function unknown
Gene Name:
shiA
Uniprot ID:
P76350
Molecular weight:
47817
Protein Details
2. Outer membrane protein N
General function:
Involved in transporter activity
Specific function:
Non-specific porin
Gene Name:
ompN
Uniprot ID:
P77747
Molecular weight:
41220
Protein Details
3. Outer membrane pore protein E
General function:
Involved in transporter activity
Specific function:
Uptake of inorganic phosphate, phosphorylated compounds, and some other negatively charged solutes
Gene Name:
phoE
Uniprot ID:
P02932
Molecular weight:
38922
Protein Details
4. Outer membrane protein F
General function:
Involved in transporter activity
Specific function:
OmpF is a porin that forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane. It is also a receptor for the bacteriophage T2
Gene Name:
ompF
Uniprot ID:
P02931
Molecular weight:
39333
Protein Details
5. Outer membrane protein C
General function:
Involved in transporter activity
Specific function:
Forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane
Gene Name:
ompC
Uniprot ID:
P06996
Molecular weight:
40368